A pattern recognition-based approach for phylogenetic network construction with constrained recombination

The tree representation of evolutionary relationship oversimplifies the view of the process of evolution as it cannot take into account the events such as horizontal gene transfer, hybridization, homoplasy and genetic recombination. Several algorithms exist for constructing phylogenetic networks which result from events such as horizontal gene transfer, hybridization and homoplasy. Very little work has been published on the algorithmic detail of phylogenetic networks with constrained recombination. The problem of minimizing the number of recombinations in a phylogenetic network, constructed using binary DNA sequences, is NP-hard. In this paper, we propose a pattern recognition-based O(n²) time approach for constructing the phylogenetic network, where n is the number of nodes or sequences in the input data. The network is constructed with the restriction that no two cycles in the network share a common node.     

Octave-tunable miniature RF resonators

The development and testing of a miniaturized, high-Q, broadly tunable resonator is described. An exemplary device, with a center frequency that is continuously tunable from 1.2 to 2.6GHz, was tested in detail. Experimental results demonstrated a resonator Q of up to 380, and typical insertion loss of -1.9dB for a 25MHz 3-dB bandwidth. These resonators have been used to stabilize a broadly-tunable oscillator with phase noise of -132dBc/Hz at 100-kHz offset, with a center frequency tunable from 1.2-2.6GHz, and a tuning speed of 1GHz/ms.     

Nitrification parameter measurement for plant design: experience and experimental issues with new methods.

Nitrification kinetics are important for process design, optimization, and capacity rating of activated sludge wastewater treatment plants. A Water Environment Research Foundation (WERF) project on Methods for Wastewater Characterization in Activated Sludge Modeling (WERF, 2003) focused significantly on the development of procedures for measuring the nitrifier maximum specific growth rate, micro(AUT). In addition, the importance of (and lack of data for) the nitrifier decay rate, b(AUT), was identified. This paper describes three bench-scale methods for measuring micro(AUT): the Low F/M SBR, Washout and High F/M methods. During the WERF project, the importance of pH and temperature control was investigated briefly; this paper summarizes further experimental work performed to address these issues. A summary of micro(AUT) measurements in a number of locations and using the different measurement techniques is provided.     

The impact of agricultural management practices on nutrient losses to water: data on the effects of soil drainage characteristics.

Against the background of increasing nutrient concentrations in Irish water bodies, this study set out to gain information on the potential of agricultural grassland to lose nutrients to water. Overland flow, flow from artificial subsurface drains and stream flow were gauged and sampled during heavy rainfall events. Dissolved reactive phosphorus (DRP), potassium (K), total ammonia (TA), and total oxidised nitrogen (TON) were measured in water samples. When the nutrient concentrations in water were examined in relation to the grassland management practices of the study catchments it emerged that soil P levels, the application of organic and inorganic fertilisers before heavy rainfall and the presence of grazing animals could all influence nutrient concentrations in surface and subsurface drainage water. Overall, the drainage characteristics of soil were found to have a considerable influence on the potential of land to lose nutrients to water.     

Precautionary information-generation in science and the law.

An information-generation system should be part of precautionary approaches to protecting the public's health and the environment. Such a system would include inventories or surveys of health and the environment, monitoring of them, as well as scoping out or scouting for threats or other harmful things that could occur and providing sentinels to try to identify threats before they materialize. I, then, suggest some ways in which such strategies could be adopted in science and the law as part of a precautionary approach. Doing more to generate information in an anticipatory way will assist implementation of the precautionary principle and help remove some of the uncertainty in environmental and public health protections.     

An array-compensated spherical reflector antenna for a very large number of scanned beams

There are many stringent demands imposed on the applications of spaceborne antenna systems. One of the most challenging demands is the generation of multiple beams with the ability to scan a very large number of beamwidths. Since the parabolic reflectors have limitations in this application, a 35-m spherical reflector antenna is proposed for a geostationary radar antenna at Ka-band (35.6 GHz) due to its inherent capability of scanning the beams to very large number of beamwidths. The utility of using planar array feeds for correcting spherical phase aberrations is investigated to overcome the performance degradation effects. Two different methodologies are developed for the array excitation coefficients determination based on phase conjugate matching and the results are compared. Using the compensating feed array, the radiation characteristics of the compensated spherical reflector are simulated for no scan and large scan cases and the results are compared with the uncompensated case to show performance improvement. In order to demonstrate the technological readiness of the concept a 1.5-m breadboard model is designed to be built for experimental measurements. Some important mechanical design tolerances and realistic array feed topologies are investigated. The antenna concept developed in this paper is advocated to be used in the next generation of geostationary satellite antenna systems for remote sensing radar applications.     

Anomalous splitting in microwave mode-beating spectra of semiconductor ring lasers

Mode-beating spectra are investigated in long-perimeter (1.028 cm) monolithically integrated multiple-quantum-well semiconductor ring lasers. The beating line near 8 GHz is found to be split into two components. With increasing pumping current, a normal component shifts to lower frequencies, while an anomalous higher-frequency component shifts in the opposite direction. It is suggested the anomalous blue-shifting line results from power-induced perturbation of the refractive index in the vicinity of a strong mode.     

A time-based energy-efficient analog-to-digital converter

Dual-slope converters use time to perform analog-to-digital conversion but require 2/sup N+1/ clock cycles to achieve N bits of precision. We describe a novel current-mode algorithm that also uses time to perform analog-to-digital conversion but requires 5N clock cycles to achieve N bits of precision via a successive subranging technique. The algorithm requires one asynchronous comparator, two capacitors, one current source, and a state machine. Amplification of two is achieved without the use of an explicit amplifier by simply doing things twice in time. The use of alternating voltage-to-time and time-to-voltage conversions provides natural error cancellation of comparator offset and delay, 1/f noise, and switching charge-injection. The use of few components and an efficient mechanism for amplification and error cancellation allow for energy-efficient operation: in a 0.35-/spl mu/m implementation, we were able to achieve 12 bit of DNL limited precision or 11 bit of thermal noise-limited precision at a sampling frequency of 31.25 kHz with 75 /spl mu/W of total analog and digital power consumption. These numbers yield a thermal noise-limited energy efficiency of 1.17 pJ per quantization level, making it one of the most energy-efficient converters to date in the 10-12 bit precision range.     

Multiple quasi-phase-matched device using continuous phase modulation of /spl chi//sup (2)/ grating and its application to variable wavelength conversion

We propose a new multiple quasi-phase-matched wavelength converter based on the continuous phase modulation of a /spl chi//sup (2)/ grating for use in variable wavelength conversion. A numerical study shows that the proposed device exhibits a high conversion efficiency, flexible design, and robust fabrication tolerance. A waveguide device fabricated by annealed proton exchange agrees well with the numerical design. Fine-tuning the device enabled us to demonstrate variable wavelength conversion between signals on the standard optical frequency grid. Using the device, we also demonstrated fast (<100 ps) wavelength switching of 4-channel 40-Gb/s signals. The obtained results clearly show that the proposed multiple quasi-phase-matched devices will be useful when constructing future flexible photonic networks.     

Dual Gabor frames: theory and computational aspects

We consider a general method for constructing dual Gabor elements different from the canonical dual. Our approach is based on combining two Gabor frames such that the generated frame-type operator S/sub g,/spl gamma// is nonsingular. We provide necessary and sufficient conditions on the Gabor window functions g and /spl gamma/ such that S/sub g,/spl gamma// is nonsingular for rational oversampling, considering both the continuous-time and the discrete-time settings. In contrast to the frame operator, the operator S/sub g,/spl gamma// is, in general, not positive. Therefore, all results in Gabor analysis that are based on the positivity of the frame operator cannot be applied directly. The advantage of the proposed characterization is that the algebraic system for computing the Gabor dual elements preserves the high structure of usual Gabor frames, leading to computationally efficient algorithms. In particular, we consider examples in which both the condition number and the computational complexity in computing the proposed dual Gabor elements decrease in comparison to the canonical dual Gabor elements.